Development of X-ray Free Electron Lasers (XFEL) opens new era in X-ray science. The full exploitation of unique properties of the XFEL radiation require challenging solutions that preserves radiation properties from a coherent, diffraction limited source under unprecedented instantaneous and average power load. We will present properties of simulated XFEL radiation such as coherence, source shape, divergence and longitudinal location inside the undulator. Recently, a construction of the LCLS II project has started as a major upgrade to the LCLS facility that will increase the average power of the XFEL up to 1 kW level. We will show how the X-ray simulations are used for minimizing thermal distortions on focusing of the LCLS II X-ray beams by 1 meter long Kirkpatrick-Baez mirrors. We will discuss and compare accuracy of simulations using different simulation methods and packages applied to focusing optics. The design of instruments should mitigate the damage to the optics caused by the tremendous instantaneous XFEL power. We will present X-ray simulation of the damage to the diffraction grating coatings and compare it with experimental results obtained at LCLS. The self-seeded mode of the LCLS operation increases temporal coherence and reduces greatly the bandwidth of the X-ray radiation. The results of time dependent X-ray simulations of the LCLS radiation passing through the seeding monochromator will be presented. We will compare two different approaches: Fourier Optics and an approach based on a dispersive system described by 6x6 pulse ray matrixes.